FlashGet has suffered from security flaws in its update mechanism which caused users to become infected with trojan viruses.[3][4]

There is also some concern about FlashGet downloading every file indicated by its FGUpdate3.ini file that is downloaded from the developer every time FlashGet is started. A malicious FGUpdate3.ini modified for exploit and introduced directly through the developer's server could cause FlashGet to download malware to the computer without alerting the user.[5]

On April 4, 2010, FlashGet 3.4 was released containing adware and other undisclosed and unauthorized Chinese applications.[6] Some of the ads were aggressively popping out of the system tray, causing much inconvenience. The installer was also converted to Chinese making it difficult for many users to install and remove the software.[7]